When studying microorganisms from a particular environment, it is rarely possible to grow individual species in the lab. This is because it is difficult to get growth conditions right for organisms from extreme environments like hot springs and radioactive waste sites. In addition, essential interspecies interactions can be difficult to reproduce, even for more mundane locales. For instance, microorganisms might provide one another with nutrients they can’t produce themselves. There’s just too much we don’t know about the nutrients, cross-species dependencies, and overall conditions required to grow many microbes in the lab. Nonetheless, the dynamics of microbial interactions and the complex mixtures of species in a given environment can have major impacts on ecological processes and are important to study.
Thankfully, scientists do have tools to probe these environmental dynamics even if they can’t grow microorganisms in a lab. One of these tools is metagenomics. This is the study of nucleic acids (DNA or RNA) isolated from organisms in a given environmental sample (technically, the study of DNA isolated from organisms in an environment is “metagenomics” and the study of RNA isolated from organisms in an environment is “metatranscriptomics” but we use “metagenomics” as a blanket term for both here). After sequencing the nucleic acids in an environmental sample, researchers can use computational techniques to identify the species those nucleic acids came from, predict the relative abundance of these species, identify proteins that they can potentially produce, and thereby infer some of the functions of these species in the microbial community. Thus metagenomics gives researchers a way to study complex biology when it is difficult to observe directly, either in the environment or in the lab.
In a previous post, we discussed how researchers use metagenomics techniques to discover new CRISPR tools, biosynthetic pathways, and even new viruses. In this post, we highlight ways that metagenomics can help researchers understand the important processes of viral transmission, wastewater treatment, and the evolution of antibiotic resistance.
Looking for viral transmission among and from game animals in china
Prior to infecting humans, many viruses infect reservoirs of vertebrate animals. Frequent interactions between humans and these animals can lead to the eventual “jump” of viruses to humans. Such jumps are the result of mutations in viral genetic material that enable the viruses to infect new kinds of cells. Viral transmissions between multiple animal species can precede these jumps as the viruses gain the ability to infect ever more hosts.
To understand, and ultimately try to prevent, the evolution of such potentially pandemic viruses, researchers would like to better understand viral transmission between animals, and from animals to humans. Toward this end, in “Virome characterization of game animals in China reveals a spectrum of emerging pathogens,” researchers used metagenomics techniques to discover what viruses are present in 18 different animal species commonly eaten as exotic foods in China.
Wan-Ting He and colleagues took fecal and respiratory samples from the animals and sequenced their RNA. They then used computational techniques to identify any viruses known to infect vertebrates. The presence of a wide variety of viral sequences in the samples provided evidence that many of the animals were indeed viral reservoirs. In fact, some viruses previously associated with one species were clearly shown to infect a different species. Some of the viruses were also closely related to viruses known to cause disease in humans or contained mutations associated with the ability to infect human cells. This work additionally revealed many previously-undescribed viruses harbored in animal hosts. Finally, the authors identified viruses with a high risk of interspecies or even human transmission. They also identified particular animals that were more likely to harbor these high-risk viruses with civets having a particularly large number of high-risk viruses.
This work reveals potential routes of viral transmission from animal reservoirs to humans and points to species that should be monitored for their potential to facilitate this spread. It’s quite striking that so many of these animals were viral reservoirs and the authors stress that the many apparent viral transmissions between species also highlight the dangers of keeping such game animals in close proximity.
Understanding parasitic microorganism dynamics in wastewater treatment plants
If you think back to your high school biology lessons, you may remember that there is a large group of single-celled eukaryotic microorganisms called protists. Although researchers often look to viruses, bacteria, and archaea in metagenomics studies, they can also use the techniques of the field to study protists and their important roles in various ecosystems.
In “Microeukaryotic gut parasites in wastewater treatment plants: diversity, activity, and removal,” Jule Freudenthal and colleagues set out to get a better understanding of how parasitic organisms are cleared from sewage in wastewater treatment plants. They used both DNA and RNA sequencing techniques to look at the make-up of microorganisms in various sections of the plants. They investigated both eukaryotic and prokaryotic microorganisms.
These researchers found that some protist parasites decreased in abundance in particular parts of the plants and that this decrease correlated with an increase in other microorganisms. The researchers, therefore, hypothesized that some parasites are eaten by other microorganisms during the wastewater treatment process. Those that decreased in abundance were potential prey for those that increased in abundance.
This research lays the groundwork for scientists to develop hypotheses about how interactions between various microorganisms lead to effective wastewater treatment. Future work could try to stimulate these interactions and thereby improve the treatment process. For instance, future researchers could use this and similar data to hypothesize what microorganisms should be added to the wastewater treatment process to increase predation on parasites and thereby lower the number of parasites in the treated product.
Tracing the development of antibiotic resistance in the mouse gut microbiome
Antibiotics are a mainstay of modern medicine. They are used to treat a wide variety of bacterial infections and prophylactically to prevent infections during surgeries and other healthcare procedures. Unfortunately, as we’ve discussed in a recent series of blog posts, many bacteria and other microorganisms have and continue to evolve resistance to antimicrobials. Indeed, it is estimated that antimicrobial resistant microbes cause millions of deaths annually.
To better understand the processes by which bacteria in the gut evolve antibiotic resistance, researchers used metagenomics to trace the types of bacteria present in mice before and after antibiotic treatment. In their work titled, “Evolution of the murine gut resistome following broad-spectrum antibiotic treatment”, Laura de Nies and colleagues followed not only how the abundance of bacterial species changed upon antibiotic treatment, but also how the quantity of various antibiotic resistance genes changed. There are a variety of ways antibiotic resistance genes can be shared between bacteria to change their abundance and these authors used metagenomics techniques to discover which were the most likely.
Specifically, these researchers used computational techniques to determine what role “mobile genetic elements” played in the sharing of antibiotic resistance. Mobile genetic elements can move antibiotic resistance genes between bacteria and facilitate the spread of resistance. They can include bacterial viruses known as phages and small circular pieces of DNA called plasmids. Phages may inadvertently move one chunk of a bacterial genome to another as they leave one host to infect another. These chunks of genetic material can occasionally carry antibiotic resistance genes. Plasmids, on the other hand, can be transferred between bacterial species independent from their genomic DNA via direct uptake from the environment or via transfer through a membranous tube called a “pilus.” The researcher’s observations indicated that, while most bacteria harbored antibiotic resistance genes within their genomes, others had resistance genes on both kinds of mobile genetic elements.
Finally, many antibiotic resistance genes were found on so-called “integrons.” Integrons are special DNA sequences that can incorporate new genes through the actions of “integrase” enzymes, which are encoded in the integron’s own DNA. Often they contain multiple antibiotic resistance genes and can be found on plasmids and other mobile genetic elements. In comparison with other genetic systems encoding antibiotic resistance genes, less is known about integrons and the authors point out that integron-based antibiotic resistance needs further study.
This work shows that antibiotic resistance evolves through a variety of mechanisms over the course of antibiotic treatment. If future researchers can develop means of inhibiting these various processes, they may be able to slow the evolution of antibiotic resistance and help fight the looming antibiotic resistance crisis.
Metagenomics as a starting point
As you can see, metagenomics makes it possible to study a wide variety of processes that are incredibly important to humans. Of course, these studies are just the beginning. They all point to research avenues that scientists can travel further down to decipher the mechanistic bases of these processes. With a better understanding of these processes and the consequences of altering them, researchers may be able to develop means of using their biological know-how to change these processes for the better!
Check out our Protein Discovery page to learn how we use metagenomics to discover new CRISPR systems.